Abstract

The orchestrated binding of transcriptional activators and repressors
to specific DNA sequences in the context of chromatin defines the
regulatory program of eukaryotic genomes. We developed a digital
approach to assay regulatory protein occupancy on genomic DNA in vivo
by dense mapping of individual DNase I cleavages from intact nuclei
using massively parallel DNA sequencing. Analysis of >23 million
cleavages across the Saccharomyces cerevisiae genome revealed
thousands of protected regulatory protein footprints, enabling de
novo derivation of factor binding motifs as well as the
identification of hundreds of novel binding sites for major
regulators. We observed striking correspondence between
nucleotide-level DNase I cleavage patterns and protein-DNA
interactions determined by crystallography. The data also yielded a
detailed view of larger chromatin features including positioned
nucleosomes flanking factor binding regions. Digital genomic
footprinting provides a powerful approach to delineate the
cis-regulatory framework of any organism with an available genome
sequence.

Data files

Source code

The shell script footprinting_run_all.sh takes as input the
tag counts, the mappability data and the locations of yeast intergenic
regions, and produces as output a list of footprints with
associated q-values. The script calls three other scripts, which are
listed below. To run the scripts, you must have Python and Matlab
installed on your system.